Crystal Structure of the L Intermediate of Bacteriorhodopsin: Evidence for Vertical Translocation of a Water Molecule during the Proton Pumping Cycle

Mechanism of a proton pump analyzed with computer simulations

“…A cytoplasmic orientation of the retinal prior to deprotonation is supported by the crystal structures of the L-state models from Refs. [5][6][7] (see iceblue and purple structures in Fig. 3a), FTIR experiments [19], and by the good agreement between the bR-L dipole moment change obtained from experiments and that computed with the L-state model structure from Ref.…”

“…Our computations indicate that prior to the first protontransfer step the retinal Schiff base likely re-orients [11]; twisted K-1M0K [3]; L-state models with different retinal geometries-1UCQ [7] and 2NTW [9]; M-state models with different retinal geometries-1M0M [10] and 1CWQ [11]. c, d Retinal bond alternation from QM and QM/MM computations on protonated (c) and unprotonated (d) retinal models.…”

“…3b). Although retinal is a flexible molecule and it samples a relatively wide range of conformations during dynamics [6,38,71,72], it is unclear if all geometries proposed in the L-state crystal structures [5][6][7][8][9] are indeed sampled during the reaction path. The significant energy barrier for retinal isomerisation from 15-trans to 15-syn [32,46] makes it unlikely that a 13-cis, 15-syn geometry [8] could be reached during the K-to-L transition [33].…”

“…1). Indeed, except for the crystal structure of a putative early-M [10], the crystal structures of the M state indicate coordinates for only one [23] or two [7,11,24] water molecules in the active site, suggesting that in M water molecules from the active site are either more mobile than before, or have relocated to other sites. Stabilization of the proton on D85 upon relocation of active-site water molecules would allow the protein to sample conformations other than when the Schiff base is protonated.…”

“…The millisecond timescale associated with the long-distance proton transfers may be required for protein conformational changes. The crystal structures of the reaction cycle intermediates indicate rather small structural rearrangements of the protein in K [3,4], L [5][6][7][8][9], and early-M [10]; there are structural rearrangements of the protein during the M-to-N [11][12][13][14][15], and N-to-O transitions [16][17][18]. The passage of the protein through the intermediate conformational states is also accompanied by changes in the number and location of internal water molecules [19,20].…”